The recent completion of the first draft of the human genome marked the beginning of post-genomic science. Genome projects have already catalyzed a new research effort that consists of systematic enumeration and quantification of all the genes and their products expressed in cells or tissue. Quantitative proteomics is an essential tool for protein analysis on a genome-wide scale and will be indispensable for identifying the functions and controls of genes. In particular, protein phosphorylation is the most important posttranslational modification and it plays a critical role in regulating protein functions and numerous biological processes. Large-scale quantitative analysis of protein phosphorylation, in particular, will be very useful in illuminating the phosphorylation networks in complex biological systems. To date, technologies for proteomics-wide analysis of protein phosphorylation have not been established. The work proposed in this application is aimed at the development of proteome technology for a rapid, sensitive, quantitative and comprehensive analysis of protein phosphorylation in complex biological samples. Once developed, such technology will be one of the technological foundations for proteomics and will be a widely applicable tool for biologists' attempts to dissect the functions of genes in their respective research areas.